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Barnosky presents statement on global environmental problems to Governor Brown

When California governor Jerry Brown challenged scientists to put global change issues into terms that political leaders can understand UCMP's Tony Barnosky stepped up. On May 23 Barnosky and colleagues presented a 30-page statement entitled Maintaining Humanity’s Life Support Systems in the 21st Century to the governor. It's a strong statement about global environmental problems and what people must do to insure the future health of the planet with signatories from 44 countries including two Nobel laureates, 33 members of the U.S. National Academy of Sciences and members of other nations' scientific academies.

 

Read more about Barnosky and other scientists' presentation to the governor at the UC Berkeley News Center.

 

Read the scientific consensus statement at the Millenium Alliance for Humanity & the Biosphere website.

Another feather in Judy Scotchmoor's cap

Our very own Judy Scotchmoor, Co-Director of Education and Outreach at the UCMP, received the 2013 Chancellor's Award for Public Service. The award honors outstanding public service by UC Berkeley undergraduates, graduate students, faculty, and staff. The Civic Engagement Award received by Judy is, in part, for her exceptional ability to develop, nurture, and leverage collaborative partnerships and resources to better engage the public with exciting and accessible science.

In a public ceremony held on May 9, 2013, at the Alumni House on campus, Judy’s leadership in the Understanding Evolution and Understanding Science websites was highlighted, as well as her efforts in Science@Cal, COPUS, and KQED Quest. Congratulations, Judy!

Judy with the Chancellor

Judy with Chancellor Birgeneau.

Judy at the podium

Photos courtesy of Bruce Cook Photography.

Finding forams in the Caldecott Tunnel

Day after day, over the course of two years, the massive tunnel borer worked its way through the sedimentary rock layers of the Berkeley Hills during the construction of the fourth bore of the Caldecott Tunnel, grinding up the rocks in the process into fist-size pieces that were later deposited outside the entrance of the tunnel. At the end of each work day, paleontologists sifted through these piles, referred to as the day’s "spoils." They were not only on the lookout for fossils of plants and animals; each day they also collected samples of the rocks for later testing for microfossils.

These samples eventually made their way into one of the prep labs of the UC Museum of Paleontology, a room that has become my second home during the spring semester of 2013. One of my jobs as a graduate student researcher on the CalTrans project is to break down and process these rock samples to look for evidence of ancient microscopic life.

Susan with boxes of matrix

Here I am in the UCMP prep lab. In the foreground are some of the microfossil samples to be processed. Photo by Pat Holroyd.

Looking at forams
Microfossils are by definition too small to be studied with the naked eye. A group of microfossils that we are particularly interested in are the Foraminifera, commonly referred to as “forams.” These single-celled amoeboid-like organisms, which are usually about the size of a sand grain, have shells, known as “tests,” often consisting of multiple chambers, arranged in a myriad of configurations. Living specimens extend strands of protoplasm from their tests in order to “communicate” with their ambient environment. This enables benthic (bottom-dwelling) forms to crawl and the planktonic (floating) forms to remain in suspension, while providing both with a means of obtaining food. Forams are common in marine environments all over the world, and their tests are often a major component of marine sediments.

Left: Drawing of the living foram Polystomella strigillata, from John H. Finley ed. Nelson's Perpetual Loose-Leaf Encyclopaedia (vol. 5) (New York, NY: Thomas Nelson and Sons, 1917); Right: © Creative Commons, Mihai Dragos

Foram tests are important fossils because they are paleoenvironmental indicators. As the tiny fossils accumulate in marine sediments they leave records that are often continuous for long geological stretches of time. By comparing the fossils to modern species, we can infer a great deal about the temperature, ocean depth, and depositional conditions that existed at the time that the organisms were living millions of years ago.

Processing the samples
In order to separate the microfossils from the shale and mudstone matrix, we first gently disaggregate the rocks by soaking them in water and adding Calgon water softener to prevent the finer sediments from clumping. If the rocks don’t readily start to disaggregate, heat and hydrogen peroxide are added. Because the shells of forams and other creatures often contain calcium carbonate we do not use acids to break down the rocks or we will dissolve the fossils at the same time!

Breaking up the matrix

Left: First stages of the process; Right: Some of the rocks in this sample are already starting to break down.

Once the rocks have completely broken down, the sediment is rinsed through a sieve with 63 micron (1 micron =0.001 mm) openings to remove silt and clay. After the residue is filtered and dried, it is ready to examine for forams under the stereomicroscope.

Sieving and drying

Left: Sieving to remove the smaller silt and clay particles; Right: Filtered samples drying in the oven.

So far the process sounds pretty straightforward, but the reality of doing science doesn’t always live up to our expectations. The first batch of samples were from the Orinda Formation; these broke down readily but revealed only a few charcoal fragments. The absence of forams was not surprising, as this unit was deposited in freshwater! I am hoping the Orinda will yield some ostracodes (another kind of microfossil), but none have been observed in the material processed thus far.

I next turned my attention to the samples collected from the definitely marine Sobrante Formation. While a few forams were noted on the surface of some partially broken-down rocks, most of the rocks did not break down at all. While experimenting with some alternative treatments on these samples, including soaking them in kerosene, I have begun to process the tunnel samples of the Claremont Formation, which is stratigraphically between the younger Orinda and older Sobrante formation, and represents the final sequence of marine deposition before emergence of the sea floor.

The first batch broke down readily with our gentle treatments and, when the results were viewed under the microscope, the sediment sample contained not only tiny pieces of coalified plants but a fair number of foraminifera shells.

Examining the dried residue

Left: Examining the dried residue under the stereomicroscope; Right: The view through the eyepiece. Each square in the grid is about 4 mm wide.

UCMP’s foram expert Ken Finger identified the three most common taxa as Martinotiella communis, Pyramidulina acuminata, and Lenticulina sp. Today this benthic association occurs on the continental slope, no shallower than 500 meters. Try to identify the three genera in the close up of the microscope photo on the left, below, based on the reference drawings on the right.

Three genera

Read other blog posts about the Caldecott Tunnel fossils:

Fossil neighbors, posted September 12, 2012
The arrival of the fossils, posted October 1, 2012
Prepping the fossils from the Caldecott Tunnel, posted May 16, 2013

All photos by Susan Tremblay except where indicated.

Prepping the fossils from the Caldecott Tunnel

For the last semester I have been lucky enough to work as the GSR (graduate student researcher) for the spring semester at the UC Museum of Paleontology fossil preparation lab (prep lab) under the supervision of our new lab manager, Jason Carr.

It has been fun getting back into the preparation role, something that I did as a job after college. The material we have to work on varies a lot which keeps the work interesting. It requires a variety of techniques, so I get to do something different nearly every day.

marine snailWhen we started this project in the fall semester we stored dozens of boxes and stacked them high at the offsite Regatta storage facility. I have gone through enough material that now all of the boxes are in the prep lab. We are making good progress but there is so much we are still unpacking! But, it is okay because sometimes we find marvelous surprises like this nearly perfect marine snail shell (at left).

We are constantly amazed at the number of different materials that the collectors used to wrap and protect the fossils. One shark tooth was even cleverly protected in a cut-up Coke bottle! I guess you use whatever you can in the field. The majority of the fossils that I am preparing are fish bones and scales — several of the formations that the Caldecott Tunnel plunges through were marine, such as the Sobrante Formation where most of our material was found. We are also finding a variety of plants, charcoal, bones of mammals from both the ocean and the land (including tiny mammal teeth, which will be the subject of a later blog), turtles, whole oyster beds, and whole rock samples that we process for marine microfossils and shells of foraminifera. These are important fossils because they allow us to address questions of climate and stratigraphy and GSR Susan Tremblay will tell you more about the preparation of those materials in her blog.

I am using some quite different techniques than Susan since most of the fossils that I am preparing are visible with the naked eye. Most of what I am doing is surprisingly low tech! It does take a lot of practice though and a good supply of patience. Some fossils are solid enough that we can use special air-powered tools like this pneumatic air scribe.

Ash using the air-scribe

Most of the marine mammal fossils are strong enough for this. The tools vibrate the rock though so more delicate fossils need to be stabilized with resins. I usually apply these with an eyedropper or gently brush them on like you can see here.

Ash applies resin to a fossil

These techniques are simple but really important if the fossils are to last in the collections until someone wants to come examine them.

I am excited to spend this time working in the lab. I love opening a new box and getting to see firsthand some of the remains of the animals that roamed over the East Bay hills. To learn about a world that existed so long ago and was so different that it had camels and rhinos living in it and then to realize that it existed right here in the East Bay? Exhilarating! Hard to picture perhaps but every fossil we unwrap brings us a little closer to visualizing that world.

Ashley Poust

Read other blog posts about the Caldecott Tunnel fossils:

Fossil neighbors, posted September 12, 2012
The arrival of the fossils, posted October 1, 2012

Photos courtesy of Ashley Poust and Jason Carr

The Looy Lab paleo detectives: Dori and Cindy at the NMNH

Cissites

A Cissites harkerianus leaf from Ellsworth County, Kansas, collected by Charles Sternberg in the late 1800s, and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Tuesday morning, February 12, 2013, Dori Contreras and Cindy Looy woke before dawn to catch a cross-country flight to Washington, DC, for a two-week visit to the Smithsonian’s National Museum of Natural History (NMNH). Originally, Cindy was going to attend a biannual workshop of the Evolution of Terrestrial Ecosystem Program. However, after Dori obtained a Sigma Xi grant to study a fossil leaf collection housed in the NMNH’s paleobotanical collections, they teamed up and turned it into a joint research excursion filled with an array of activities.

Dori: My main goal was to collect data for a study on the leaf characteristics of early flowering plants from a warm wet climate approximately 100 million years ago. And just to clarify, what I mean by "data" is photographs — lots and lots of high-resolution photographs of individual fossil leaves preserved in rock. The specific fossils that I was interested in come from the Fort Harker locality in Kansas. They were collected over a roughly 30-year period (1860s through 1890s) as a part of the US Geological Survey’s explorations of the geology of the Western Interior of the United States.

I wasn’t exactly sure how many specimens I would find in the museum "stacks," which consist of rows and rows of floor-to-ceiling cabinets filled with drawers of fossils. Based on Leo Lesquereux’s publications from the late 19th century, I was expecting somewhere around 100 specimens. However, after two days of opening wooden drawers I located just over 300 Fort Harker specimens! Many have never been figured or mentioned in publications, and most have not been reevaluated in over 100 years.

Dori with the camera setup

Dori photographing the Cretaceous Fort Harker flora. (photo by Cindy Looy)

I knew that it would be a major task to photograph them all in the detail needed for study, so I went right to work. The museum's imaging room had an impressive setup of top-notch, stand-mounted cameras connected to computers for remote shooting. Most of my time was spent carting specimens back and forth between the stacks and imaging room and doing nonstop photography. The trickiest part of imaging for data collection was getting the lighting angle and brightness just right to pick up the three-dimensional (and often obscure) features of each leaf. At least magnification wasn't an issue — the resolution of the camera I used was so high that a microscope was not necessary!

Inga

Inga cretaceum, another fossil leaf collected by Charles Sternberg and identified by Leo Lesquereux. Specimen from the Department of Paleobiology, National Museum of Natural History. (photo by Dori Contreras)

Ultimately, I was able to photograph almost every specimen in the collection, totaling a whopping 50 gigabytes of images. Now I look forward to the next tasks: naming and organizing all those files, followed by detailed measuring of key ecological leaf characteristics for each specimen. Luckily ,a new Undergraduate Research Apprentice Program (URAP) student just joined "Team Contreras." We hope this study will provide insight into the structure and function of plant communities in warm, wet climates during the early radiation of flowering plants.

Cindy: Last year, members of the NMNH's Evolution of Terrestrial Ecosystem Program received good news from NSF: their Research Coordination Network proposal, "Synthesizing deep time and recent community ecology," was funded. This means that over the next five years a group of paleo- and "extant" ecologists will meet semiannually to study the assembly and disassembly of biological communities in the past and present. Attending this winter's edition of our meeting series was my main goal of this museum trip. Our workshop consisted of three days of presentations, data gathering and subsequent analyses in a friendly and inspiring atmosphere.

Workshop attendees

The NMNH’s Evolution of Terrestrial Ecosystems Program workshop attendees. Cindy is ninth from the left. (photo by Dori Contreras)

It is always a treat to return to the NMNH, smack in the middle of the National Mall in DC. From 2004 to 2008 I worked as a research fellow in the Paleobiology Department of this bigger sister of the UCMP and being at the NMNH always instills a special feeling. It could be the 325,000 square feet of exhibition space, the 20,000 daily visitors from all over the globe, or the 126,000,000 documented specimens in the museum's collections. Perhaps it is the illusion of being in the "center of the world," with the close proximity of the NMNH to the White House. But still, I know how lucky I am to be at the west coast equivalent of the NMNH. The UCMP public exhibits may be primarily online, but with the Department of Integrative Biology, the UCMP boasts something that the NMNH lacks altogether and something that presidential fly-bys can never compensate for: a pack of fabulous graduate and undergraduate students!

Outside of the meeting I had plenty of time to catch up with friends and work with former colleagues. Fellow-paleobotanist Bill DiMichele and I spent quite a bit of time in the museum's paleobotany collections. During the past 20 years, Paleozoic paleobotanists from the NMNH (Bill DiMichele, Dan Chaney, and Serge Mamay) have intensively sampled latest Pennsylvanian, Early Permian and Middle Permian sites in Texas. More than 360 collections of compression fossils were assembled using sampling strategies appropriate for the reconstruction of plant communities. Bill and I pulled out numerous conifers for morphotyping. We are trying to get a grip on how diverse early Permian Euramerican forests were, and how seed-plant dominated assemblages changed through time. Working our way through all the cabinets took quite some time, but that's nothing compared to all the imaging and measuring that still needs to be done. Ah well, that’s what is great about being a scientist: the work is never completed. Every question answered raises plenty of new, interesting questions.

Bill and Cindy

Cindy and Bill DiMichele working in the paleobotanical collections. (photo by Dori Contreras)

Both: Additionally, we got to present our work to east coast paleontologists and geologists at the annual Penn-Smithsonian Geobiology Symposium. It's always good to foster cross-talk on the continental scale and represent the paleontological force that is the UCMP!

Cindy and Dori sample pie

If you ever find yourself in DC, we highly recommend breakfast at Paul's French bakery ("Bonjour Madame!"). Here we test some of their pies for Cindy’s birthday. (photo by Bill DiMichele)

Reports from Regatta: Two Cal Alumni and the USGS Menlo Park Collection

Nelson letter and envelope

The letter from Cliff Nelson to Warren Addicott.
 

As undergraduate work-study students recataloging the United States Geological Survery (USGS) Menlo Park Invertebrate collection at the UCMP, we've come across the names Nelson and Addicott time and time again in extensive database entries or on the original, yellowing locality cards paired with each specimen. The names of the paleontologists and geologists responsible for collecting these fossils in the Menlo Park collection are largely unknown to us, but found immersed within the aging drawers of the invertebrate fossils were several curious and antiquarian documents that have brought these names to life. One recently discovered letter, written by UC Berkeley alumnus Cliff Nelson records his activities in the collections during the summer of 1974.

In the letter, Nelson discusses his dissertation work that focused on migration patterns of Neptunea, a large sea snail indigenous to the North Pacific. While studying the migration traces of Neptunea through the North Pacific and to the North Atlantic and California Current, Nelson proposed to elevate Neptunea beyond the level of subgenus. His dissertation interpreted Neptunea as a genus, with the inclusion of 56 named species — half of which are extinct. The letter goes on to explain Nelson's use of the Menlo Park collection and the late nights he spent scavenging through the collections, searching for invertebrate specimens to support his dissertation.

The letter also delivers some insights on other individuals who played an important role in Nelson's research. Warren Addicott, the recipient of Nelson's letter (and another popular name found often in the Menlo Park Collection), obtained his doctorate at UC Berkeley in 1956 and led a distinguished scientific career at the US Geological Survey. The letter concludes with Nelson's gracious thanks to Addicott for his help with his dissertation and an acknowledgment to Dr. Stearns McNeil, another familiar name associated with the Menlo Park collection and the USGS.

After receiving his Ph.D. from UC Berkeley in 1974, the year the letter was written, Nelson went on to publish over fifty articles in refereed journals and books. His work primarily focused on the history of scholarship, ideas, and institutions in natural sciences. Currently, Nelson works as a geologist and historian at the USGS. In 2011 he received the Friedman Distinguished Service Award from the Geological Society of America's History and Philosophy of Geology Division.

Letters such as this one help us discover the identities of the names we come upon so frequently. This is just one of many documents that shines light on the Menlo Park collection and allows us to reconstruct the UC Museum of Paleontology's historic and scientific past.

Neptuneidae specimens

USGS gastropod specimens (Family Neptuneidae) studied by Nelson during the course of his doctoral study at UC Berkeley. Left: A specimen from USGS Cenozoic Locality M863 Pliocene, Gubick Formation of Alaska, Colville River. Right: A specimen identified by Nelson as Beringius beringii; from USGS Cenozoic Locality M860 Pleistocene, Gubik Formation near Point Barrow village, Alaska. Both specimens were collected by John O'Sullivan pre-1960.

The Looy Lab paleo detectives

Solving the mysteries of the past and present one rock at a time

East of the Berkeley campus, we see the beautiful, green Berkeley Hills, the golden letter "C" and a somewhat classy-looking, dome-shaped building on the Lawrence Berkeley National Laboratory campus. This houses the ALS, or Advanced Light Source. Personally, I find the name a bit silly because it doesn't seem to capture the awesomeness of this giant machine. It's like calling the Space Shuttle a Progressive Flying Tool.

synchotron at LBL

Photo from newscenter.lbl.gov

The ALS is a synchrotron, a particular type of particle accelerator. The particles are sped up by a shifting magnetic field within a closed circuit. The shape of this circuit is an almost circular polygon and since the building was specifically designed for the synchrotron, the building is round. But what happens inside?

Each time when the particle beam is bent at each of the polygon's corners, light is produced — primarily ultraviolet and x-rays. The x-rays are not your ordinary dental office x-rays, but much "harder" x-rays. Unlike the relatively harmless photo at the tooth doctor, this beam would kill you before you could say "¿qué?"

But what can paleontologists and paleobotanists do with this advanced light? Hard x-rays allow us to see fossils while they are still inside the rock. This means that you don't have to crack open the rocks, clear away rock matrix and run the risk of damaging precious fossils. In some cases, the material is simply too fragile to be prepared; it would not hold up. Scanning the rock allows us to make 3D reconstructions of fossils hidden inside the rock without damaging them.

We've been scanning all kinds of really old fossils: horsetails from the Carboniferous (~300 million years ago, or Ma), kelp holdfasts from the Oligocene (~30 Ma), tiny (3 mm or ~1/8 inch) and not so tiny (7 cm or ~2¾ inch) pine cones, early land plants from the Devonian (~390 Ma), and pollen cones of extinct redwoods from the Cretaceous (~70 Ma). The size of the fossils is limited by the size of the protective shielding enclosure that keeps the scientists safe while using these lethal x-rays.

Because the cyclotron basically runs 24/7, the scanning time slots are generally 24 hours long and scanning rocks can take a while. Here's the general process that we go through for each scan:

Cindy and Ivo

Left: First, we select a fossil. Right: Then we mount it on a stand (improvising a la MacGyver). These and the rest of the photos are by Cindy Looy and Dori Lynne Contreras.

Orienting a fossil on the stand

Next we orient the fossil on the stand just right to get the best quality scan of the target specimen (which surprisingly takes a bit of work and "expert guess-timation").

The hutch

Once ready, the mount and fossil are placed in a "hutch" made of radiation shielding. Left: This is the hutch, a big container that protects everyone around from the harmful x-rays. Right: Inside the hutch there is a normal optical camera (at ~9 o'clock), the stand on which the fossil is mounted, and the x-ray detector (the big black box at the right).

The hutch doors and camera

To start the scanning process a number of safety procedures have to be followed, otherwise the beamline will not open. Left: The doors of the hutch have to be closed, and while an ominous alarm sounds, you have to press certain buttons to actually allow the x-ray to come into the hutch. Once it does, a red rotating emergency light comes on and the doors cannot be opened. Right: Once the sample is in the hutch we use the normal camera to focus in on the sample.

Adjusting the settings and set to go

Left: As each fossil sample is different, adjustments to the settings are needed. For instance, thicker rocks generally need a higher dose of x-rays than thin ones. Right: And we are good to go! It's scanning time!

Waiting for the scan to finish

And then, we wait …

Data analysis and celebration

Left: Actually, there is not a whole lot of sitting about going on, because the data that the x-ray collector gathers has to be analyzed. This takes up quite a bit of time (note the ridiculous amount of caffeine) and a LOT of computing power. Luckily, the computers at Lawrence Berkeley National Lab are up to the task! Right: Then we celebrate our success!

Darwin Day Roadshow

Lisa's presentation

Lisa White makes her presentation to Mrs. Ball's 7th grade class at the Urban Promise Academy in Oakland. Photo by Alison Ball.
 

It is not unusual to see evolutionary biologists around the world involved in celebration activities on February 12th — the reason? Charles Darwin's birthday! UCMP and the National Evolutionary Synthesis Center (NESCent) are no exception and this year the activities overlapped. Two years ago, NESCent initiated the Darwin Day Roadshow in order to bring evolutionary science to schools and museums around the country. This year, Lisa White was asked by NESCent to bring the Roadshow to Urban Promise Academy, a small Oakland Unified School District middle school serving students in the Fruitvale neighborhood of Oakland, CA. Presenting to Ms. Alison Ball's 7th grade classroom on February 15, 2013, Lisa highlighted research at the UCMP, profiling examples of evolution from the Understanding Evolution website, while conveying why the science of evolution is important and relevant.

To the enjoyment of the students, Lisa brought in an array of fossils for the students to touch and see the tangible evidence for evolution up close. Lisa also spoke about her own education and training, what it is like to be a paleontologist, and how she came to work at the UCMP. Lisa said "the students were such an inspiration and their enthusiasm and eagerness to learn more about paleontology suggests the next generation of potential scientists are alive and well in classrooms like Urban Promise Academy."

Caldwell's rare octopus research makes headlines

Roy Caldwell has been working with Richard Ross of the California Academy of Sciences to study a rare, beautiful, and so far unnamed species of octopus. Their work, along with some of Roy's photos, is the subject of a feature article in the San Francisco Chronicle.

New bone histology book from UCMP and UC Press

The University of California Press has just published Bone Histology of Fossil Tetrapods: Advancing methods, analysis, and interpretation. The book represents the proceedings of an NSF-sponsored workshop and is the first comprehensive summary of the field of fossil bone histology. The twelve authors of the various chapters cover topics ranging from basic bone biology to calculating and analyzing the evolution of growth rates in bones, in addition to step-by-step instructions for setting up a hard tissue histology lab and processing specimens.

The microstructure of bone has a great deal to tell us about the biology of ancient vertebrates. The patterns of how bone tissue was deposited and the configuration of the blood canals in the bone provide a very good idea of how fast the animal was growing, and how its growth regime changed through life. Growth lines, deposited annually like tree rings, help us to calculate how old animals were when they died and even when they matured sexually. These data in turn give us information about life history strategies and metabolic regimes.

UCMP alum Andrew Lee and grad student Sarah Werning were two of the many contributors to the volume who have benefited from studying UCMP’s fossil collections. UCMP researchers have been in the forefront of fossil bone histology for decades, and our histology lab continues to be one of the most active research areas of the Museum. The book was edited by Kevin Padian of UCMP and Ellen-Thérèse Lamm of the Museum of the Rockies.